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bioRxiv · 10.1101/364810

DoubletDecon: Cell-State Aware Removal of Single-Cell RNA-Seq Doublets

DePasquale, E. A. K.·Schnell, D. J.·Valiente, I.·Blaxall, B. C.·Grimes, H. L.·Singh, H.·Salomonis, N.
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Abstract

Methods for single-cell RNA sequencing (scRNA-Seq) have greatly advanced in recent years. While droplet- and well-based methods have increased the capture frequency of cells for scRNA-Seq, these technologies readily produce technical artifacts, such as doublet-cell and multiplet-cell captures. Doublets occurring between distinct cell-types can appear as hybrid scRNA-Seq profiles, but do not have distinct transcriptomes from individual cell states. We introduce DoubletDecon, an approach that detects doublets with a combination of deconvolution analyses and the identification of unique cell-state gene expression. We demonstrate the ability of DoubletDecon to identify synthetic and cell-hashing cell singlets and doublets from scRNA-Seq datasets of varying cellular complexity. DoubletDecon is able to account for cell-cycle effects and is compatible with diverse species and unsupervised population detection algorithms (e.g., ICGS, Seurat). We believe this approach has the potential to become a standard quality control step for the accurate delineation of cell states.

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DePasquale, E. A. K., Schnell, D. J., Valiente, I., Blaxall, B. C., Grimes, H. L., Singh, H., Salomonis, N.. 2018-07-08. DoubletDecon: Cell-State Aware Removal of Single-Cell RNA-Seq Doublets. https://doi.org/10.1101/364810

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